topo_ic_sim_term {GAPGOM} | R Documentation

## GAPGOM - topo_ic_sim_term()

### Description

Algorithm to calculate similarity between two GO terms.

### Usage

    topo_ic_sim_term(organism, ontology, go1, go2, go_data = NULL)

### Arguments

`organism` | where to be scanned genes reside in, this option is neccesary to select the correct GO DAG. Options are based on the org.db bioconductor package; http://www.bioconductor.org/packages/release/BiocViews.html#___OrgDb Following options are available: "fly", "mouse", "rat", "yeast", "zebrafish", "worm", "arabidopsis", "ecolik12", "bovine", "canine", "anopheles", "ecsakai", "chicken", "chimp", "malaria", "rhesus", "pig", "xenopus".
`ontology` | desired ontology to use for similarity calculations. One of three; "BP" (Biological process), "MF" (Molecular function) or "CC" (Cellular Component).
`go1` | GO term of first term.
`go2` | GO term of second term.
`go_data` | prepared go_data, from the set_go_data function. It is practically the same as in GOSemSim, but with a slightly nicer interface.

### Details

This function is made for calculating topological similarity of two GO terms in the GO DAG structure. The topological similarity is based on edge weights and information content (IC). [1]

### Value

TopoICSim score between the two terms.

### References

[1] Ehsani R, Drablos F: TopoICSim: a new semantic similarity measure based on gene ontology. BMC Bioinformatics 2016, 17(1):296)

### Examples

    result <- topo_ic_sim_term("human", "MF", "GO:0018478", "GO:0047105")

[Package GAPGOM version 1.0.0 Index]